From e2df8e7c0f73e0ff22caa8fe14851cfdcf500f6a Mon Sep 17 00:00:00 2001 From: "Markus J. Ankenbrand" Date: Thu, 13 Sep 2018 14:10:44 +0200 Subject: [PATCH] seaview: init at 4.7 (#46595) --- .../science/biology/seaview/default.nix | 41 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 + 2 files changed, 43 insertions(+) create mode 100644 pkgs/applications/science/biology/seaview/default.nix diff --git a/pkgs/applications/science/biology/seaview/default.nix b/pkgs/applications/science/biology/seaview/default.nix new file mode 100644 index 00000000000..17cf903ae49 --- /dev/null +++ b/pkgs/applications/science/biology/seaview/default.nix @@ -0,0 +1,41 @@ +{ stdenv, fetchurl, coreutils, fltk, libjpeg }: + +stdenv.mkDerivation rec { + version = "4.7"; + name = "seaview-${version}"; + + src = fetchurl { + url = "ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_${version}.tar.gz"; + sha256 = "0fhyq7dcn0izhwcfin9ajsr7kmmsqm9f1np1rmhzg4digfwqb29n"; + }; + + buildInputs = [ fltk libjpeg ]; + + patchPhase = "sed -i 's#PATH=/bin:/usr/bin rm#'${coreutils}/bin/rm'#' seaview.cxx"; + installPhase = "mkdir -p $out/bin; cp seaview $out/bin"; + + meta = with stdenv.lib; { + description = "GUI for molecular phylogeny"; + longDescription = '' + SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. + - SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees. + - SeaView drives programs muscle or Clustal Omega for multiple sequence alignment, and also allows to use any external alignment algorithm able to read and write FASTA-formatted files. + - Seaview drives the Gblocks program to select blocks of evolutionarily conserved sites. + - SeaView computes phylogenetic trees by + + parsimony, using PHYLIP's dnapars/protpars algorithm, + + distance, with NJ or BioNJ algorithms on a variety of evolutionary distances, + + maximum likelihood, driving program PhyML 3.1. + - Seaview can use the Transfer Bootstrap Expectation method to compute the bootstrap support of PhyML and distance trees. + - SeaView prints and draws phylogenetic trees on screen, SVG, PDF or PostScript files. + - SeaView allows to download sequences from EMBL/GenBank/UniProt using the Internet. + + Seaview is published in: + + Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 27(2):221-224. + ''; + homepage = http://doua.prabi.fr/software/seaview; + license = licenses.gpl3; + maintainers = [ maintainers.iimog ]; + platforms = platforms.linux; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index b644c531f32..7deebde25b2 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -20729,6 +20729,8 @@ with pkgs; strelka = callPackage ../applications/science/biology/strelka { }; + seaview = callPackage ../applications/science/biology/seaview { }; + varscan = callPackage ../applications/science/biology/varscan { }; hmmer = callPackage ../applications/science/biology/hmmer { };